How to determine the molecular volume of a docked complex?

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Abolfazl Barzegar

You can use Spdbv software. It is useful for this aim.

Abolfazl Noorjahan

Would you please specify more precisely what you mean by molecular volume?

You are looking for occupied volume of your system? You are looking for free volume of your system?

Your are looking for average available volume for your proteins? And .....

E.g. You can tell us what do you want to do with this volume!

Cheers

Chhavi Dawar

hi Abolfazl i want to determine the average available volume of the docked complex.

Rachid Charbel Maroun

CASTp determines only the volume of the cavities it finds, not the total volume. For that purpose use UCSF Chimera. First calculate the surface of your molecule with the menu Actions Surface. Then, there are plenty of volume functions in the menu Tools Surface/Binding Analysis.

Cheers,

thanks Rachid ,that was a grt help.